Core analysis code for RICOPILI can be found at https://sites.google.com/a/broadinstitute.org/ricopili/. This includes PLINK (https://www.coggenomics.org/plink2/), EIGENSOFT (https://www.hsph.harvard.edu/alkes-price/software/), Eagle2 (https://alkesgroup.broadinstitute.org/Eagle/), Minimac3 (https://genome.sph.umich.edu/wiki/Minimac3), SHAPEIT3 (https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html), METAL (https://genome.sph.umich.edu/wiki/METAL_Documentation) and LDSR (https://github.com/bulik/ldsc). MAGMA can be found at https://ctg.cncr.nl/software/magma. Genomic SEM, specifically the tutorial ‘Models without Individual SNP effects’ can be found here: https://github.com/GenomicSEM/GenomicSEM/wiki/3.-Models-without-Individual-SNPeffects
